Proteomic profiling of protein expression changes after 3 months-exercise in ESRD patients on hemodialysis

Abstract

The prevalence of chronic kidney disease (CKD) is steadily increasing, and it is a global health burden. Exercise has been suggested to improve physical activity and the quality of life in patients with CKD, eventually reducing mortality. This study investigated the change in physical performance after exercise in dialysis-dependent patients with CKD and analyzed differentially expressed proteins before and after the exercise. Plasma samples were collected at enrollment and after 3 months of exercise. Liquid chromatography with tandem mass spectrometry analysis and data-independent acquisition results were analyzed to determine the significantly regulated proteins. A total of 37 patients on dialysis were recruited, and 16 were randomized to exercise for 3 months. The hand grip strength and the walking speed significantly improved in the exercise group. Proteome analysis revealed 60 significantly expressed proteins after 3 months of exercise. In the protein functional analysis, the significantly expressed proteins were involved in the immune response. Also, some of the key significantly expressed proteins [(M Matrix metallopeptidase 9 (MMP-9), Activin A Receptor Type 1B (ACVR1B), Fetuin B (FETUB)] were validated via an enzyme-linked immunosorbent assay. Our results showed that exercise in dialysis-dependent patients with CKD could improve their physical performance. These results indicated that this beneficial effect of exercise in these populations could be associated with immune response.

Keywords: Chronic kidney disease; End-stage renal disease; Proteomics; hemodialysis.

Fig. 1

Schematic diagram summarizing the study design. (A) Total 37 patients were recruited and 16 were randomized for 3 months exercise during each hemodialysis session. (B) The plasma samples for proteomic analysis were collected at the enrollment time and 3 months later in exercise group. The LC-MS/MS analysis methods was performed and the DIA data from individual samples were analyzed to determine significantly regulated protein. The bioinformatics analysis was used for protein functional annotation and protein–protein interaction. (C) To validate proteome data, the ELISA analysis was used for plasma sample of exercise group. The change of protein expression levels was also compare to the sample from age-matched healthy controls

Fig. 2

Plasma proteins that differentially expressed in before exercise and after 3 months exercise (A) Volcano plot shows the fold changes and associated P – values. (Dashed line indicates significance threshold, P = 0.05). (B) The concentration scale for 60 significantly differentially expressed proteins, which were converted from the quantitative data based on MS analysis

Fig. 3

The KEGG pathway and GO analysis of significantly expressed proteins. The vertical axis represents the pathway category and the horizontal axis represents the enrichment score [− log(P-value)] of the pathway. Significantly enriched pathways (P < 0.05) are presented. The data were analyzed by DAVID bioinformatics tools. (A) The top 24 most functionally enriched KEGG pathways found in before exercise vs. after 3 months exercise. (B) The top 30 enriched GO terms found in before exercise vs. after 3 months exercise.

Fig. 4

The protein–protein interaction network analysis was performed using Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) software. The nodes reflect individual proteins enriched in the analysis, and the edges are the functional associations based on various online resources. (A) Protein-Protein interaction network of significantly expressed proteins that contains 58 nodes and 153 edges, with a PPI enrichment P-value < 1.0 x 10^− 16, line thickness indicates the strength of data support (The thickest edge indicates the highest confidence in protein-protein interaction). (B) Protein-Protein interaction network of top 10 proteins that contains 14 nodes and 15 edges, with a PPI enrichment P-value < 0.008, line color indicates the type of interaction evidence (light blue,known interactions from curated databases; purple, known interactions experimentally determined; green, gene neighborhood; red, gene fusions Blue, gene co-occurrence.)

Fig. 5

Validation of proteomics results with ELISA. Age-matched healthy control, before exercise, and after 3 months exercise. *P < control vs. before exercise; **P < control vs. before exercise; ***P < before exercise vs. after exercise. Control, Age-matched healthy control; before, before exercise in dialysis patients; after, after 3 months exercise in dialysis patients